Re: Variogram not plotting and problem with pattern function

From: Butler, David <David.Butler_at_DEEDI.QLD.GOV.AU>
Date: Fri, 22 Jan 2010 09:36:57 +1000

Fernando, The "pattern" argument to coef.asreml() is designed to extract the coefficients for interaction terms, is those involving ":", such as "Column_*:Row_*". The "list" argument returns the coefficients in a named list, so you can get just those coefficients for the "ped" term via the appropriate list element. I cannot reproduce the error in plotting the variogram with my test data set, would you be kind enough to forward me your data file, suitably disguised if necessary? Dave. ________________________________ From: ASReml users discussion group [mailto:ASREML-L@DPI.NSW.GOV.AU] On Behalf Of grignola Sent: Friday, 22 January 2010 7:06 AM To: ASREML-L@DPI.NSW.GOV.AU Subject: Variogram not plotting and problem with pattern function Hello, A couple of questions. 1. I upgraded to asreml 3.0 and I'm running the model: met.1.asr <- asreml(yld ~ Site, random =~ diag(Site):geno, rcov=~at(Site):ar1(Column):ar1(Row), data=mmData). The sample data is nicely balanced. 1 2 3 4 5 6 SITE1 72 72 72 72 72 72 SITE2 72 72 72 72 72 72 SITE3 72 72 72 72 72 72 However, with this 3.0 version I cannot plot the variogram as I used to with the previous version. I now get an error: > plot(variogram(met.1.asr)) Error in `$<`(`*tmp*`, "gamma", value = c(0, 0.415962583409219, : replacement has 1296 rows, data has 0 2. To extract solutions from a simple genetic model fitting pedigree as "random =~ ped(Pedigree)". coef(model1.asr)$random effect ped(Pedigree)_GARDEL_URUGUAYO 2.23904 I first tried this code: coef(model1.asr,pattern='ped(Pedigree)'), but it does not work. It returns just the name of the effect, but no solutions. However, I noticed that the following code does work (note that 'ped(' is missing) coef(model1.asr,pattern='Pedigree)') Are there any rules that I'm missing when using "pattern"? It looks like it does not like "(" Thanks for you for your assistance. Fernando -------------------- m2f -------------------- Sent using Mail2Forum ( Read this topic online here: -------------------- m2f -------------------- This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation. ********************************DISCLAIMER**************************** The information contained in the above e-mail message or messages (which includes any attachments) is confidential and may be legally privileged. It is intended only for the use of the person or entity to which it is addressed. If you are not the addressee any form of disclosure, copying, modification, distribution or any action taken or omitted in reliance on the information is unauthorised. Opinions contained in the message(s) do not necessarily reflect the opinions of the Queensland Government and its authorities. If you received this communication in error, please notify the sender immediately and delete it from your computer system network.
Received on Fri Jan 22 2010 - 09:36:57 EST

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